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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ), 'gf_id' => 'HOM05D001158', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001158' ), 'data_identifier' => 'HOM05D001158', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001158', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '533', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p04460' => 'bna', 'A09p13530' => 'bna', 'A09p15600' => 'bna', 'A09p48410' => 'bna', 'Aa31LG10G10510' => 'aar', 'Aa31LG2G670' => 'aar', 'Aa31LG5G510' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.173' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.177' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.178' => 'aag', 'Actinidia10012' => 'ach', 'Actinidia13147' => 'ach', 'Actinidia27526' => 'ach', 'Actinidia38303' => 'ach', 'Ah.05g176320' => 'amhyb', 'Ah.12g057380' => 'amhyb', 'AL2G12160' => 'aly', 'AL2G12190' => 'aly', 'AL5G36620' => 'aly', 'Aqoxy4G02886' => 'aox', 'Aqoxy4G02887' => 'aox', 'Aqoxy4G02888' => 'aox', 'Aqoxy4G02889' => 'aox', 'Aqoxy5G03960' => 'aox', 'Aqoxy7G00312' => 'aox', 'Aqoxy7G00386' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C2IL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2V00G0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YAK67' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34Z14Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53HUJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZWF51' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LFR1QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPK9E2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LVS803' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV03GU' => 'arhy', 'AT1G63220' => 'ath', 'AT3G55470' => 'ath', 'AT4G00467' => 'ath', 'ATR0680G051' => 'atr', 'ATR0680G245' => 'atr', 'Atru.chr12.437' => 'acertr', 'Atru.chr12.438' => 'acertr', 'Atru.chr5.435' => 'acertr', 'Atru.chr5.492' => 'acertr', 'Atru.chr8.370' => 'acertr', 'AUR62004307' => 'cqu', 'AUR62004355' => 'cqu', 'AUR62010599' => 'cqu', 'AUR62012096' => 'cqu', 'AUR62017241' => 'cqu', 'AUR62022540' => 'cqu', 'AUR62022560' => 'cqu', 'AUR62022758' => 'cqu', 'AUR62037283' => 'cqu', 'AUR62039370' => 'cqu', 'BcaB01g00097' => 'bca', 'BcaB02g08418' => 'bca', 'BcaB07g31392' => 'bca', 'BcaC02g09760' => 'bca', 'BcaC04g22477' => 'bca', 'BcaC04g22712' => 'bca', 'BcaC07g39866' => 'bca', 'BolC4t25254H' => 'bol', 'BolC8t50688H' => 'bol', 'BolC9t52976H' => 'bol', 'BolC9t54517H' => 'bol', 'BolC9t54787H' => 'bol', 'BraA04t16157Z' => 'bra', 'BraA09t37004Z' => 'bra', 'BraA09t37200Z' => 'bra', 'BraA09t40293Z' => 'bra', 'C04p36880' => 'bna', 'C08p30720' => 'bna', 'C09p16020' => 'bna', 'C09p18850' => 'bna', 'CAN.G72.7' => 'can', 'CAN.G786.7' => 'can', 'CAN.G859.6' => 'can', 'CAN.G91.1' => 'can', 'CANSAT21G1256' => 'cansat', 'CANSAT56G0809' => 'cansat', 'CANSAT56G0861' => 'cansat', 'CANSAT56G0931' => 'cansat', 'CANSAT56G1341' => 'cansat', 'CANSAT56G2755' => 'cansat', 'CANSAT56G3988' => 'cansat', 'CARHR000050' => 'chi', 'CARHR048260' => 'chi', 'CARHR165490' => 'chi', 'CARHR165500' => 'chi', 'CARHR165510' => 'chi', 'CARHR248570' => 'chi', 'Carub.0002s0162' => 'cru', 'Carub.0005s2219' => 'cru', 'Carub.0006s3679' => 'cru', 'Ca_05892_v3' => 'car', 'Ca_05893_v3' => 'car', 'Ca_12825_v3' => 'car', 'Ca_25782_v3' => 'car', 'CBR_g51509' => 'cbr', 'Cc00_g12190' => 'ccan', 'Cc02_g07750' => 'ccan', 'Cc06_g02580' => 'ccan', 'Cc08_g14260' => 'ccan', 'CDE02G4597' => 'cde', 'CDE04G3749' => 'cde', 'CDE09G0205' => 'cde', 'CDE09G0348' => 'cde', 'CDE09G0461' => 'cde', 'CDE09G0487' => 'cde', 'CDE09G0724' => 'cde', 'CDE09G0857' => 'cde', 'CDE11G0813' => 'cde', 'Cfa001467' => 'cfa', 'Cfa012134' => 'cfa', 'Cfa017369' => 'cfa', 'Ciclev10022928m.g' => 'ccl', 'Ciclev10024048m.g' => 'ccl', 'Ciclev10024188m.g' => 'ccl', 'Ciclev10032979m.g' => 'ccl', 'CiPaw.01G056000' => 'cil', 'CiPaw.01G288200' => 'cil', 'CiPaw.02G030600' => 'cil', 'CiPaw.02G184700' => 'cil', 'CiPaw.11G138800' => 'cil', 'ClCG01G002980' => 'cla', 'ClCG05G001540' => 'cla', 'ClCG09G019700' => 'cla', 'COL.COLO4_15057' => 'col', 'COL.COLO4_34421' => 'col', 'Cpa.g.sc1.414' => 'cpa', 'Cpa.g.sc1.415' => 'cpa', 'Cpa.g.sc18.207' => 'cpa', 'Cre02.g076050' => 'cre', 'CsaV3_3G008920' => 'csa', 'CsaV3_5G003090' => 'csa', 'CsaV3_5G026720' => 'csa', 'CSS0028507' => 'camsi', 'CSS0029556' => 'camsi', 'CSS0037686' => 'camsi', 'DCAR_006754' => 'dca', 'DCAR_008414' => 'dca', 'DCAR_011712' => 'dca', 'DCAR_024062' => 'dca', 'DCAR_025192' => 'dca', 'DCAR_027610' => 'dca', 'DCAR_028744' => 'dca', 'Dinv03041' => 'din', 'Dinv26024' => 'din', 'Dinv35594' => 'din', 'Dinv37167' => 'din', 'Dinv43775' => 'din', 'Duzib068G0027' => 'dzi', 'Duzib114G0179' => 'dzi', 'Duzib133G0578' => 'dzi', 'Duzib138G0797' => 'dzi', 'Duzib205G0316' => 'dzi', 'ECA236G2829' => 'eca', 'ECA238G1861' => 'eca', 'ECA240G1030' => 'eca', 'ECA248G2659' => 'eca', 'EL10Ac1g00419' => 'bvu', 'EL10Ac1g00518' => 'bvu', 'EL10Ac2g04739' => 'bvu', 'EL10Ac5g12762' => 'bvu', 'Eucgr.E00562' => 'egr', 'Eucgr.J00003' => 'egr', 'FAN01G0761' => 'fan', 'FAN01G1962' => 'fan', 'FAN01G3010' => 'fan', 'FAN03G0977' => 'fan', 'FAN03G1858' => 'fan', 'FAN03G2312' => 'fan', 'FAN03G2416' => 'fan', 'FAN03G3434' => 'fan', 'FAN04G0969' => 'fan', 'FAN04G1507' => 'fan', 'FAN05G1968' => 'fan', 'FAN06G0707' => 'fan', 'FAN06G3042' => 'fan', 'FAN06G3401' => 'fan', 'FAN06G3873' => 'fan', 'FAN06G4028' => 'fan', 'FAN08G0932' => 'fan', 'FAN09G0889' => 'fan', 'FAN10G0224' => 'fan', 'FAN10G0809' => 'fan', 'FAN10G2554' => 'fan', 'FAN10G3581' => 'fan', 'FAN13G0905' => 'fan', 'FAN14G4771' => 'fan', 'FAN18G2374' => 'fan', 'FvH4_5g01841' => 'fve', 'FvH4_5g01850' => 'fve', 'FvH4_6g13620' => 'fve', 'FvH4_7g13480' => 'fve', 'FvH4_7g13490' => 'fve', 'FvH4_7g13491' => 'fve', 'FvH4_7g13500' => 'fve', 'FvH4_7g14250' => 'fve', 'FvH4_7g22610' => 'fve', 'Glyma.02G247900' => 'gma', 'Glyma.02G248000' => 'gma', 'Glyma.02G248100' => 'gma', 'Glyma.03G009400' => 'gma', 'Glyma.03G015400' => 'gma', 'Glyma.05G204900' => 'gma', 'Glyma.07G075300' => 'gma', 'Glyma.08G011900' => 'gma', 'Glyma.11G219000' => 'gma', 'Glyma.14G068400' => 'gma', 'Glyma.14G068451' => 'gma', 'Glyma.18G038400' => 'gma', 'Glyma.18G224800' => 'gma', 'Gohir.A08G179700' => 'ghi', 'Gohir.A10G220100' => 'ghi', 'Gohir.A11G021600' => 'ghi', 'Gohir.A12G109100' => 'ghi', 'Gohir.D08G198500' => 'ghi', 'Gohir.D10G229600' => 'ghi', 'Gohir.D10G230000' => 'ghi', 'Gohir.D11G021300' => 'ghi', 'Gohir.D12G112100' => 'ghi', 'Gorai.004G209300' => 'gra', 'Gorai.007G022600' => 'gra', 'Gorai.008G121500' => 'gra', 'Gorai.011G262100' => 'gra', 'Gorai.011G262500' => 'gra', 'GSVIVG01016533001' => 'vvi', 'GSVIVG01019850001' => 'vvi', 'GSVIVG01026929001' => 'vvi', 'GSVIVG01034164001' => 'vvi', 'HanXRQChr03g0084481' => 'han', 'HanXRQChr06g0169771' => 'han', 'HanXRQChr06g0170051' => 'han', 'HanXRQChr07g0201291' => 'han', 'HanXRQChr07g0201311' => 'han', 'HanXRQChr07g0201321' => 'han', 'HanXRQChr13g0406941' => 'han', 'Haze_08913' => 'cav', 'Haze_08916' => 'cav', 'Haze_15201' => 'cav', 'Haze_17075' => 'cav', 'Haze_20802' => 'cav', 'Hma1.2p1_0033F.1_g020460' => 'hma', 'Hma1.2p1_0953F.1_g241140' => 'hma', 'HPP92_005037' => 'vpl', 'HPP92_019354' => 'vpl', 'HPP92_020864' => 'vpl', 'HPP92_028125' => 'vpl', 'Hund16081' => 'sun', 'Hund16082' => 'sun', 'Hund16949' => 'sun', 'Hund27312' => 'sun', 'Lalb_Chr05g0224981' => 'lal', 'Lalb_Chr10g0097311' => 'lal', 'Lalb_Chr10g0104551' => 'lal', 'Lalb_Chr16g0389801' => 'lal', 'Lalb_Chr17g0339651' => 'lal', 'Lalb_Chr17g0339911' => 'lal', 'Lalb_Chr17g0346211' => 'lal', 'Lalb_Chr17g0346221' => 'lal', 'Lalb_Chr19g0127161' => 'lal', 'Lj1g0006347' => 'lja', 'Lj1g0022489' => 'lja', 'Lj3g0001533' => 'lja', 'Lj3g0016409' => 'lja', 'Lj3g0027208' => 'lja', 'Lj4g0028152' => 'lja', 'LjContig00141g0001022' => 'lja', 'Lsat_1_v5_gn_2_119260' => 'lsa', 'Lsat_1_v5_gn_5_154020' => 'lsa', 'Lsat_1_v5_gn_6_86780' => 'lsa', 'Lsat_1_v5_gn_7_4640' => 'lsa', 'Lsat_1_v5_gn_7_5481' => 'lsa', 'Lsat_1_v5_gn_8_135021' => 'lsa', 'Manes.01G064500' => 'mes', 'Manes.02G025000' => 'mes', 'Manes.05G034500' => 'mes', 'Manes.07G116900' => 'mes', 'Mapoly0021s0033' => 'mpo', 'Mapoly0021s0067' => 'mpo', 'MBI05_g28391_MAGBIO' => 'mbi', 'MBI17_g21050_MAGBIO' => 'mbi', 'MD01G1048800' => 'mdo', 'MD01G1048900' => 'mdo', 'MD01G1049000' => 'mdo', 'MD01G1060400' => 'mdo', 'MD01G1135100' => 'mdo', 'MD06G1076700' => 'mdo', 'MD07G1137300' => 'mdo', 'MD07G1199800' => 'mdo', 'MD12G1142700' => 'mdo', 'MD14G1098100' => 'mdo', 'Medtr1g008930' => 'mtr', 'Medtr1g008950' => 'mtr', 'Medtr5g079880' => 'mtr', 'Medtr5g079890' => 'mtr', 'Medtr7g075960' => 'mtr', 'Medtr8g030870' => 'mtr', 'Medtr8g032300' => 'mtr', 'Medtr8g032320' => 'mtr', 'MELO3C005646.2' => 'cme', 'MELO3C006112.2' => 'cme', 'MELO3C021622.2' => 'cme', 'MELO3C021623.2' => 'cme', 'Migut.B01751' => 'egut', 'Migut.E01118' => 'egut', 'Migut.F00781' => 'egut', 'Migut.F01446' => 'egut', 'Migut.F01486' => 'egut', 'Migut.F01488' => 'egut', 'Migut.F01490' => 'egut', 'Migut.N01425' => 'egut', 'Migut.O00554' => 'egut', 'MSTRG.13833' => 'ama', 'MSTRG.27371' => 'ama', 'MSTRG.28211' => 'ama', 'MSTRG.4871' => 'ama', 'Nitab4.5_0000134g0160' => 'nta', 'Nitab4.5_0000386g0070' => 'nta', 'Nitab4.5_0003154g0040' => 'nta', 'Nitab4.5_0003486g0010' => 'nta', 'Nitab4.5_0003604g0020' => 'nta', 'Nitab4.5_0007064g0020' => 'nta', 'Nitab4.5_0010166g0030' => 'nta', 'Nitab4.5_0013552g0030' => 'nta', 'Nitab4.5_0014068g0010' => 'nta', 'Nitab4.5_0017742g0010' => 'nta', 'Nn1g01415' => 'nnu', 'Nn2g11121' => 'nnu', 'Nn2g11122' => 'nnu', 'Nn2g11123' => 'nnu', 'Nn2g11124' => 'nnu', 'Nn2g13359' => 'nnu', 'Nn6g33545' => 'nnu', 'Oeu035184.1' => 'oeu', 'Oeu048239.1' => 'oeu', 'Oeu048240.1' => 'oeu', 'Oeu049558.2' => 'oeu', 'Oeu053462.1' => 'oeu', 'Oeu056345.1' => 'oeu', 'Oeu060666.1' => 'oeu', 'Oeu061931.1' => 'oeu', 'Os01g0841700' => 'osa', 'Os02g0640000' => 'osa', 'Os04g0531100' => 'osa', 'Os04g0682100' => 'osa', 'Peaxi162Scf00008g02130' => 'pax', 'Peaxi162Scf00102g01417' => 'pax', 'Peaxi162Scf00233g00911' => 'pax', 'Peaxi162Scf00233g01013' => 'pax', 'Peaxi162Scf00658g00838' => 'pax', 'Peaxi162Scf00714g00121' => 'pax', 'Peaxi162Scf00760g00325' => 'pax', 'PGR031G0433' => 'pgr', 'PGR042G3504' => 'pgr', 'PGR044G0934' => 'pgr', 'PGSC0003DMG400003045' => 'stu', 'PGSC0003DMG400019943' => 'stu', 'PGSC0003DMG400026887' => 'stu', 'PGSC0003DMG400027742' => 'stu', 'Phvul.002G286900' => 'pvu', 'Phvul.008G073400' => 'pvu', 'Phvul.008G232600' => 'pvu', 'Phvul.008G232700' => 'pvu', 'Phvul.008G232800' => 'pvu', 'Phvul.010G093800' => 'pvu', 'Phvul.010G098601' => 'pvu', 'Potri.002G155600' => 'ptr', 'Potri.010G203000' => 'ptr', 'Potri.010G203100' => 'ptr', 'Potri.014G084100' => 'ptr', 'Pp3c19_4390' => 'ppa', 'Pp3c2_4180' => 'ppa', 'Pp3c6_180' => 'ppa', 'Prupe.2G158500' => 'ppe', 'Prupe.2G158600' => 'ppe', 'Prupe.2G158700' => 'ppe', 'Prupe.2G158800' => 'ppe', 'Prupe.2G159000' => 'ppe', 'Prupe.2G170300' => 'ppe', 'Prupe.2G236500' => 'ppe', 'Prupe.5G094600' => 'ppe', 'Prupe.5G094700' => 'ppe', 'Prupe.6G256400' => 'ppe', 'Psat2g041360' => 'psa', 'Psat2g041560' => 'psa', 'Psat4g153120' => 'psa', 'Psat4g153240' => 'psa', 'Psat4g153320' => 'psa', 'Psat6g005920' => 'psa', 'PSO017G1357' => 'pso', 'PSO063G0717' => 'pso', 'PSO170G1080' => 'pso', 'PSO339G1358' => 'pso', 'PSO339G1600' => 'pso', 'PSO339G2505' => 'pso', 'PSO339G3088' => 'pso', 'PSO339G3324' => 'pso', 'PSO339G3661' => 'pso', 'PSO339G3820' => 'pso', 'PSO339G5943' => 'pso', 'PSO384G0441' => 'pso', 'PSO384G0672' => 'pso', 'PSO384G1026' => 'pso', 'PSO384G1042' => 'pso', 'PSO384G1915' => 'pso', 'PSO384G4587' => 'pso', 'PSO478G2347' => 'pso', 'PSO541G1198' => 'pso', 'PSO541G2545' => 'pso', 'PSO541G2863' => 'pso', 'PSO541G4238' => 'pso', 'PSO541G4880' => 'pso', 'PSO675G0399' => 'pso', 'PSO675G1703' => 'pso', 'PSO675G4373' => 'pso', 'PSO675G8934' => 'pso', 'PSO782G4020' => 'pso', 'PSO801G0504' => 'pso', 'QL05p059673' => 'qlo', 'QL07p048450' => 'qlo', 'QL07p048538' => 'qlo', 'QL08p048848' => 'qlo', 'QL08p049802' => 'qlo', 'QL08p050047' => 'qlo', 'QL08p059642' => 'qlo', 'QL12p017881' => 'qlo', 'RcHm_v2.0_Chr1g0352961' => 'rch', 'RcHm_v2.0_Chr1g0352971' => 'rch', 'RcHm_v2.0_Chr1g0352981' => 'rch', 'RcHm_v2.0_Chr1g0353001' => 'rch', 'RcHm_v2.0_Chr1g0353011' => 'rch', 'RcHm_v2.0_Chr1g0353021' => 'rch', 'RcHm_v2.0_Chr1g0353061' => 'rch', 'RcHm_v2.0_Chr1g0355241' => 'rch', 'RcHm_v2.0_Chr1g0367731' => 'rch', 'RcHm_v2.0_Chr7g0198671' => 'rch', 'RcHm_v2.0_Chr7g0198681' => 'rch', 'RcHm_v2.0_Chr7g0198691' => 'rch', 'Rhsim04G0157600' => 'rsi', 'Rhsim07G0015300' => 'rsi', 'Rhsim07G0019300' => 'rsi', 'RhsimUnG0042000' => 'rsi', 'Sabra02G0123400' => 'sbr', 'Sabra08G0041200' => 'sbr', 'Sabra10G0156700' => 'sbr', 'Sabra14G0061100' => 'sbr', 'Sabra15G0062800' => 'sbr', 'SalBow3G2992' => 'sbo', 'SalBow3G3197' => 'sbo', 'SalBow3G4032' => 'sbo', 'SalBow5G0008' => 'sbo', 'SalBow5G4972' => 'sbo', 'SalBow6G6219' => 'sbo', 'Sc02g0002150' => 'sci', 'Sc26g0000920' => 'sci', 'Sed0001831' => 'sed', 'Sed0011042' => 'sed', 'Sed0015047' => 'sed', 'Sed0020915' => 'sed', 'Sed0021975' => 'sed', 'SEGI_00426' => 'sgi', 'SEGI_17910' => 'sgi', 'SEGI_18461' => 'sgi', 'SEGI_18496' => 'sgi', 'SEGI_24006' => 'sgi', 'SEGI_24227' => 'sgi', 'SEGI_30600' => 'sgi', 'SGA_v2.0_scaffold43G16448' => 'sas', 'SGA_v2.0_scaffold4G02324' => 'sas', 'SHI13444' => 'shi', 'SMO147G0403' => 'smo', 'SMO343G0034' => 'smo', 'Solyc04g011540.4' => 'sly', 'Solyc08g080680.4' => 'sly', 'Solyc10g017480.1' => 'sly', 'Solyc10g018035.1' => 'sly', 'Solyc10g018050.2' => 'sly', 'Solyc10g018060.2' => 'sly', 'Sopen04g005720' => 'spe', 'Sopen08g028990' => 'spe', 'Sopen10g007070' => 'spe', 'Sopen10g007080' => 'spe', 'Sopen10g007100' => 'spe', 'Sp2g01320' => 'spa', 'Sp5g07000' => 'spa', 'Sp6g00510' => 'spa', 'TAR375G1126' => 'tar', 'TAR629G2983' => 'tar', 'TAR633G1883' => 'tar', 'THA.LOC104801440' => 'tha', 'THA.LOC104809411' => 'tha', 'THA.LOC104823579' => 'tha', 'THA.LOC104824277' => 'tha', 'Thecc.01G359300' => 'tca', 'Thecc.03G274700' => 'tca', 'Thecc.10G040600' => 'tca', 'Thhalv10010786m.g' => 'esa', 'Thhalv10023745m.g' => 'esa', 'Thhalv10029141m.g' => 'esa', 'TPR.G12096' => 'tpr', 'TPR.G3464' => 'tpr', 'TPR.G3507' => 'tpr', 'TPR.G39880' => 'tpr', 'TPR.G9808' => 'tpr', 'TWI15G0357' => 'twi', 'TWI38G1521' => 'twi', 'TWI59G0723' => 'twi', 'TWI60G1600' => 'twi', 'unitig_0.g1229' => 'ugi', 'unitig_0.g1230' => 'ugi', 'unitig_0.g1265' => 'ugi', 'unitig_32.g10682' => 'ugi', 'unitig_748.g7109' => 'ugi', 'unitig_88.g27758' => 'ugi', 'vmacro07177' => 'vma', 'vmacro08650' => 'vma', 'vmacro13288' => 'vma', 'vmacro13322' => 'vma', 'VMungo0251G1334' => 'vmu', 'VMungo0331G0755' => 'vmu', 'VMungo0647G0930' => 'vmu', 'VMungo0647G1461' => 'vmu', 'VMungo0647G2054' => 'vmu', 'Zm00001eb075700' => 'zma', 'Zm00001eb148310' => 'zma', 'Zm00001eb185780' => 'zma', 'Zm00001eb192950' => 'zma', 'Zm00001eb433960' => 'zma' ) $gf_id = 'HOM05D001158' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001158' ) $data_identifier = 'HOM05D001158' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 10, 'bca' => (int) 7, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 6, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 25, 'fve' => (int) 9, 'gma' => (int) 13, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 10, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 10, 'psa' => (int) 6, 'pso' => (int) 29, 'qlo' => (int) 8, 'rch' => (int) 12, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433960' $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